From: Harish Vashisth (harish.vashisth_at_gmail.com)
Date: Fri Jun 20 2014 - 14:07:31 CDT
Dear NAMD Users and Developers:
We have recently installed NAMD2.9 from source on our CRAY machine (Machine
configuration given here:
http://trillian-use.sr.unh.edu/index.php/Main_Page.) Regular NAMD jobs are
working fine, however, we are not able to load shared object files using
"load" command under NAMD config. file. For example, making use of a
tclforces script like this; this is the simplest possible example we have
tried which was created using tcl/swig.
###################################
puts " loading shared object"
load ./example.so example
set ans [pow 3 4]
puts "ANS: $ans "
puts "Shared object working"
proc calcforces { } {
print "inside calcforces"
}
################################
The error we get when jobs crash is: dynamic loading is not currently
available on this system.
Looking here (http://wiki.tcl.tk/9830), we found that it is likely due to
unavailability of a functional load command.
Not sure if we missed anything imp. during installation?
Previously on other Linux clusters, we have been able to successfully use
above example and it works fine on a local workstation as well. Even on
CRAY, loading the example.so under "tclsh" from terminal works fine.
Here are some more details on two different ways we have tried installing
NAMD, and both gave same dynamic loading not available error:
[Not all of these modules are needed]
module switch PrgEnv-cray PrgEnv-gnu
module load rca
module load craype-hugepages8M
module load ugni
module add gni-headers
module add csa
Charm++ from prior build:
./build charm++ gemini_gni-crayxe smp --with-production -j16
From current build:
env MPICXX=mpicxx \
./build charm++ mpi-crayxe smp -j32 --with-production
NAMD
config line from prior build:
./config CRAY-XT-g++ --charm-arch gemini_gni-crayxe-smp
From current build:
./config CRAY-XT-g++ --charm-arch mpi-crayxe-smp
Jobs are run using following command in a PBS script:
aprun -n ${NUMPROCS} -cc none
/home/rcc/rea/NAMD_2.9_Source/CRAY-XT-g++/namd2 $CONFFILE >& $LOGFILE
Any help/suggestions are appreciated. Thanks.
-----------------------
Harish Vashisth
Assistant Professor
Department of Chemical Engineering
University of New Hampshire, Durham, NH 03824
Phone: (603)-862-2483
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